Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_011841670.1 RSPH17029_RS12340 threonine-phosphate decarboxylase CobD
Query= curated2:Q1LT68 (360 letters) >NCBI__GCF_000015985.1:WP_011841670.1 Length = 324 Score = 81.3 bits (199), Expect = 3e-20 Identities = 68/225 (30%), Positives = 104/225 (46%), Gaps = 21/225 (9%) Query: 33 LNANEYPQPTFYMLRSSNLNRYPDCQPQELLNSYAAYAGVQPNQVLACRGADEGIELLIR 92 +N YP P L + L PD + L + A A +LA GA I+L+ R Sbjct: 29 INRVPYPMPP---LPARALTALPDAAAEARLLAAARLAFRTEAPMLAVAGAQAAIQLVPR 85 Query: 93 TFCEPSKDKILFCPPTYGMYRVSAETFGVAYCAIQALDNWQLDLDTIYAQLDCVKLIYIC 152 P + ++L PTY + S G WQ++ + A L+ L + Sbjct: 86 -LTPPGRARVL--GPTYNEHAASLRAAG-----------WQVEEVSELAALEGADLAVLV 131 Query: 153 HPNNPTGNIINPSDIRQLLDITHGRTILVVDEAYIDFYPTASISSWINHYPHLVILRTLS 212 +PNNP G P +R LL GR L+VDE++ D P S++ P L++LR+ Sbjct: 132 NPNNPDGRRHPPEALRALLPRV-GR--LLVDESFGDPLPDLSLAPEAG-VPGLLVLRSFG 187 Query: 213 KAFALAGLRCGFILANPDIIKLLLKVIAPYPISRPVVDIAKQALS 257 K + LAGLR GF+L N + + L ++ P+ +S P + AL+ Sbjct: 188 KFYGLAGLRLGFVLGNAEDVAALARMAGPWAVSGPAIAAGTVALA 232 Lambda K H 0.323 0.138 0.428 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 228 Number of extensions: 10 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 360 Length of database: 324 Length adjustment: 29 Effective length of query: 331 Effective length of database: 295 Effective search space: 97645 Effective search space used: 97645 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 16 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory